From f16dc66d64522eafaeb90c63a0ad86012ff56482 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 7 Sep 2018 16:19:37 +0200
Subject: [PATCH] unknown entries are also cached
---
.../annotation/services/TaxonomyBackend.java | 370 +++++++++---------
1 file changed, 188 insertions(+), 182 deletions(-)
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java
index 5ab139112c..e85f29d76d 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java
@@ -23,187 +23,193 @@ import lcsb.mapviewer.model.map.MiriamType;
*/
public class TaxonomyBackend extends CachableInterface implements IExternalService {
- /**
- * Constant defining human taxonomy.
- */
- public static final MiriamData HUMAN_TAXONOMY = new MiriamData(MiriamType.TAXONOMY, "9606");
-
- /**
- * Prefix string used for marking the query in database as query by taxonomy
- * term.
- */
- static final String TAXONOMY_CACHE_PREFIX = "TAXONOMY_TERM: ";
-
- /**
- * Prefix string used for marking queries in database as queries returning
- * name by taxonomy id.
- */
- static final String TAXONOMY_NAME_CACHE_PREFIX = "TAXONOMY_NAME_BY_ID: ";
-
- @Override
- public String refreshCacheQuery(Object query) throws SourceNotAvailable {
- String result = null;
- try {
- if (query instanceof String) {
- String name = (String) query;
- if (name.startsWith(TAXONOMY_CACHE_PREFIX)) {
- String term = name.substring(TAXONOMY_CACHE_PREFIX.length());
- MiriamData md = getByName(term);
- if (md != null) {
- result = md.getResource();
- }
- } else if (name.startsWith(TAXONOMY_NAME_CACHE_PREFIX)) {
- String id = name.substring(TAXONOMY_NAME_CACHE_PREFIX.length());
- result = getNameForTaxonomy(new MiriamData(MiriamType.TAXONOMY, id));
- } else if (name.startsWith("http")) {
- result = getWebPageContent(name);
- } else {
- throw new InvalidArgumentException("Don't know what to do with query: " + query);
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- } catch (TaxonomySearchException | IOException e) {
- throw new SourceNotAvailable(e);
- }
- return result;
- }
-
- /**
- * Returns {@link MiriamData} representing taxonomy identified by name.
- *
- * @param term
- * name of the organism
- * @return {@link MiriamData} representing taxonomy
- * @throws TaxonomySearchException
- * thrown when there is a problem with accessing taxonomy database
- */
- public MiriamData getByName(String term) throws TaxonomySearchException {
- if (term == null || "".equals(term.trim())) {
- return null;
- }
- String res = getCacheValue(TAXONOMY_CACHE_PREFIX + term);
- if (res != null) {
- return new MiriamData(MiriamType.TAXONOMY, res);
- }
- try {
-
- String queryTerm = term.trim();
- if (queryTerm.indexOf("(") >= 0) {
- queryTerm = queryTerm.substring(0, queryTerm.indexOf("("));
- }
- if (queryTerm.toUpperCase().startsWith("C.")) {
- queryTerm = "Caenorhabditis" + queryTerm.substring(2);
- } else if (queryTerm.toUpperCase().startsWith("D.")) {
- queryTerm = "Drosophila" + queryTerm.substring(2);
- } else if (queryTerm.toUpperCase().startsWith("P.")) {
- queryTerm = "Pristionchus" + queryTerm.substring(2);
- } else if (queryTerm.toUpperCase().startsWith("T.")) {
- queryTerm = "Tribolium" + queryTerm.substring(2);
- } else if (queryTerm.equalsIgnoreCase("Mouse")) {
- queryTerm = "Mus musculus";
- } else if (queryTerm.equalsIgnoreCase("Rat")) {
- queryTerm = "Rattus norvegicus";
- }
- queryTerm = URLEncoder.encode(queryTerm, "UTF-8");
- String url = "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&name=" + queryTerm;
- String page = getWebPageContent(url);
- Pattern idPattern = Pattern.compile("Taxonomy ID: ([0-9]+)");
- Matcher matcher = idPattern.matcher(page);
- if (!matcher.find()) {
- logger.warn("Unknown organism: " + term);
- return null;
- } else {
- String name = matcher.group(1);
- setCacheValue(TAXONOMY_CACHE_PREFIX + term, name);
- return new MiriamData(MiriamType.TAXONOMY, name);
- }
- } catch (IOException e) {
- throw new TaxonomySearchException("Problem with accessing taxonomy database", e);
- }
-
- }
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(TaxonomyBackend.class);
-
- /**
- * Default constructor.
- */
- public TaxonomyBackend() {
- super(TaxonomyBackend.class);
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus(MiriamType.TAXONOMY.getCommonName(), MiriamType.TAXONOMY.getDbHomepage());
-
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
-
- try {
- MiriamData md = getByName("human");
- if (md == null) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- } else if (md.equals(TaxonomyBackend.HUMAN_TAXONOMY)) {
- status.setStatus(ExternalServiceStatusType.OK);
- } else {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- }
- } catch (Exception e) {
- logger.error(MiriamType.TAXONOMY.getCommonName() + " is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
-
- /**
- * Returns name for given taxonomy id.
- *
- * @param miriamData
- * object representing taxonomy id
- * @return name for given taxonomy id
- * @throws TaxonomySearchException
- * thrown when there is a problem with accessing external database
- */
- public String getNameForTaxonomy(MiriamData miriamData) throws TaxonomySearchException {
- if (miriamData == null) {
- return null;
- }
- String res = getCacheValue(TAXONOMY_NAME_CACHE_PREFIX + miriamData.getResource());
- if (res != null) {
- return res;
- }
-
- try {
- String url = "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=" + miriamData.getResource();
- String page = getWebPageContent(url);
- Pattern idPattern = Pattern.compile("<title>Taxonomy browser \\(([A-Za-z0-9\\ \\.]+)\\)</title>");
- Matcher matcher = idPattern.matcher(page);
- if (!matcher.find()) {
- logger.warn("Unknown organism: " + miriamData);
- return null;
- } else {
- String name = matcher.group(1);
- setCacheValue(TAXONOMY_NAME_CACHE_PREFIX + miriamData.getResource(), name);
- return name;
- }
- } catch (IOException e) {
- throw new TaxonomySearchException("Problem with accessing taxonomy database", e);
- }
- }
-
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
+ /**
+ * Constant defining human taxonomy.
+ */
+ public static final MiriamData HUMAN_TAXONOMY = new MiriamData(MiriamType.TAXONOMY, "9606");
+
+ /**
+ * Prefix string used for marking the query in database as query by taxonomy
+ * term.
+ */
+ static final String TAXONOMY_CACHE_PREFIX = "TAXONOMY_TERM: ";
+
+ /**
+ * Prefix string used for marking queries in database as queries returning name
+ * by taxonomy id.
+ */
+ static final String TAXONOMY_NAME_CACHE_PREFIX = "TAXONOMY_NAME_BY_ID: ";
+
+ @Override
+ public String refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String result = null;
+ try {
+ if (query instanceof String) {
+ String name = (String) query;
+ if (name.startsWith(TAXONOMY_CACHE_PREFIX)) {
+ String term = name.substring(TAXONOMY_CACHE_PREFIX.length());
+ MiriamData md = getByName(term);
+ if (md != null) {
+ result = md.getResource();
+ }
+ } else if (name.startsWith(TAXONOMY_NAME_CACHE_PREFIX)) {
+ String id = name.substring(TAXONOMY_NAME_CACHE_PREFIX.length());
+ result = getNameForTaxonomy(new MiriamData(MiriamType.TAXONOMY, id));
+ } else if (name.startsWith("http")) {
+ result = getWebPageContent(name);
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with query: " + query);
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ } catch (TaxonomySearchException | IOException e) {
+ throw new SourceNotAvailable(e);
+ }
+ return result;
+ }
+
+ /**
+ * Returns {@link MiriamData} representing taxonomy identified by name.
+ *
+ * @param term
+ * name of the organism
+ * @return {@link MiriamData} representing taxonomy
+ * @throws TaxonomySearchException
+ * thrown when there is a problem with accessing taxonomy database
+ */
+ public MiriamData getByName(String term) throws TaxonomySearchException {
+ if (term == null || "".equals(term.trim())) {
+ return null;
+ }
+ String res = getCacheValue(TAXONOMY_CACHE_PREFIX + term);
+ if (res != null) {
+ if (res.equals("null")) {
+ return null;
+ } else {
+ return new MiriamData(MiriamType.TAXONOMY, res);
+ }
+ }
+ try {
+
+ String queryTerm = term.trim();
+ if (queryTerm.indexOf("(") >= 0) {
+ queryTerm = queryTerm.substring(0, queryTerm.indexOf("("));
+ }
+ if (queryTerm.toUpperCase().startsWith("C.")) {
+ queryTerm = "Caenorhabditis" + queryTerm.substring(2);
+ } else if (queryTerm.toUpperCase().startsWith("D.")) {
+ queryTerm = "Drosophila" + queryTerm.substring(2);
+ } else if (queryTerm.toUpperCase().startsWith("P.")) {
+ queryTerm = "Pristionchus" + queryTerm.substring(2);
+ } else if (queryTerm.toUpperCase().startsWith("T.")) {
+ queryTerm = "Tribolium" + queryTerm.substring(2);
+ } else if (queryTerm.equalsIgnoreCase("Mouse")) {
+ queryTerm = "Mus musculus";
+ } else if (queryTerm.equalsIgnoreCase("Rat")) {
+ queryTerm = "Rattus norvegicus";
+ }
+ queryTerm = URLEncoder.encode(queryTerm, "UTF-8");
+ String url = "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&name=" + queryTerm;
+ String page = getWebPageContent(url);
+ Pattern idPattern = Pattern.compile("Taxonomy ID: ([0-9]+)");
+ Matcher matcher = idPattern.matcher(page);
+ if (!matcher.find()) {
+ logger.warn("Unknown organism: " + term);
+ setCacheValue(TAXONOMY_CACHE_PREFIX + term, "null");
+ return null;
+ } else {
+ String name = matcher.group(1);
+ setCacheValue(TAXONOMY_CACHE_PREFIX + term, name);
+ return new MiriamData(MiriamType.TAXONOMY, name);
+ }
+ } catch (IOException e) {
+ throw new TaxonomySearchException("Problem with accessing taxonomy database", e);
+ }
+
+ }
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(TaxonomyBackend.class);
+
+ /**
+ * Default constructor.
+ */
+ public TaxonomyBackend() {
+ super(TaxonomyBackend.class);
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus(MiriamType.TAXONOMY.getCommonName(),
+ MiriamType.TAXONOMY.getDbHomepage());
+
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+ MiriamData md = getByName("human");
+ if (md == null) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ } else if (md.equals(TaxonomyBackend.HUMAN_TAXONOMY)) {
+ status.setStatus(ExternalServiceStatusType.OK);
+ } else {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ }
+ } catch (Exception e) {
+ logger.error(MiriamType.TAXONOMY.getCommonName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+ /**
+ * Returns name for given taxonomy id.
+ *
+ * @param miriamData
+ * object representing taxonomy id
+ * @return name for given taxonomy id
+ * @throws TaxonomySearchException
+ * thrown when there is a problem with accessing external database
+ */
+ public String getNameForTaxonomy(MiriamData miriamData) throws TaxonomySearchException {
+ if (miriamData == null) {
+ return null;
+ }
+ String res = getCacheValue(TAXONOMY_NAME_CACHE_PREFIX + miriamData.getResource());
+ if (res != null) {
+ return res;
+ }
+
+ try {
+ String url = "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=" + miriamData.getResource();
+ String page = getWebPageContent(url);
+ Pattern idPattern = Pattern.compile("<title>Taxonomy browser \\(([A-Za-z0-9\\ \\.]+)\\)</title>");
+ Matcher matcher = idPattern.matcher(page);
+ if (!matcher.find()) {
+ logger.warn("Unknown organism: " + miriamData);
+ return null;
+ } else {
+ String name = matcher.group(1);
+ setCacheValue(TAXONOMY_NAME_CACHE_PREFIX + miriamData.getResource(), name);
+ return name;
+ }
+ } catch (IOException e) {
+ throw new TaxonomySearchException("Problem with accessing taxonomy database", e);
+ }
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
}
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